Revision as of 17:47, 10 April 2013

Introduction

Before a research group can use LSDYNA on sharcnet, a license must be purchased directly from LSTC for the sharcnet license server. Alternately, if a research group resides at a institution that has sharcnet computing hardware (mac, uwo, guelph, waterloo) it maybe possible to use a pre-existing site license hosted on an accessible institutional license server.

Usage

These usage instructions apply to the module based installation of lsdyna found under directory /opt/sharcnet/lsdyna on licensed clusters shown in the above Availability Table. To access and use this software you must be a member of the lsdyna group. Users who belong to a licensed department will be given a 5 digit port number. The value should then be inserted into the appropriate departmental export statement before loading the module file as follows:

o UWO Civil and Environmental Engineering Dept

export LSTC_LICENSE_SERVER='PortNumber'@license1.uwo.sharcnet

o McGill Mechanical Engineering Department

export LSTC_LICENSE_SERVER='PortNumber'@license2.uwo.sharcnet

o UW Mechanical and Mechatronics Engineering Dept

export LSTC_LICENSE_SERVER='PortNumber'@license3.uwo.sharcnet

Module Selection

[roberpj@orc-login1:~] module avail lsdyna
 
-------------------------------------- /opt/sharcnet/modules ---------------------------------------
lsdyna/ls971mpp6.0.0 lsdyna/ls971mpp6.1.1 lsdyna/ls971smp6.1.0 lsdyna/ls980mppB1
lsdyna/ls971mpp6.1.0 lsdyna/ls971smp6.0.0 lsdyna/ls971smp6.1.1 lsdyna/ls980smpB1

o For serial or threaded jobs, using ls971 do:

module load lsdyna/ls971smp6.1.1

o For mpi jobs, using ls971 do:

module unload intel openmpi lsdyna
module load intel/11.1.069 openmpi/intel/1.5.4 lsdyna/ls971mpp6.1.1

o For serial or threaded jobs, using version ls980 do:

module load lsdyna/ls980smpB1

o For mpi jobs, using version ls980 do:

module unload intel openmpi lsdyna
module load intel/12.1.3 openmpi/intel/1.4.5 lsdyna/ls980mppB1

Job Submission

To run the single or double precision solvers specify lsdyna_s or lsdyna_d respectively:

o SUBMIT 1CPU SERIAL JOB

sqsub -r 7d -q serial -o ofile.%J --mpp=2G lsdyna_d i=airbag.deploy.k ncpu=1 

o SUBMIT 4CPU SMP JOB

sqsub -r 7d -q threaded -n 4 -o ofile.%J --mpp=2G lsdyna_d i=airbag.deploy.k ncpu=4

o SUBMIT 4CPU MPI JOB

sqsub -r 7d -q mpi -n 4 -o ofile.%J --mpp=1G lsdyna_d i=airbag.deploy.k

Example Job

STEP1) The following shows a sample sqsub jobs submission for the airbag example to the mpi queue as shown in this link http://www.dynaexamples.com/examples-manual/misc/airbag:

cp -a /opt/sharcnet/lsdyna/ls971smp6.1.1/examples /work/$USER/test-lsdyna
cd /work/$USER/test-lsdyna/misc/airbag
gunzip airbag.deploy.k.gz
module unload intel openmpi lsdyna
module load intel/11.1.069 openmpi/intel/1.5.4 lsdyna/ls971mpp6.1.1
export LSTC_LICENSE_SERVER=#####@license#.uwo.sharcnet
sqsub -r 1h -q mpi --mpp=4G -n 8 -o ofile.%J lsdyna_d i=airbag.deploy.k

STEP2) With the job still running, use the following echo command to trigger generation of restart files at which point the file D3KIL will vanish:

echo "sw3" > D3KIL

STEP3) Now either manually kill off the job or wait until it exceeds the -r time limit:

sqkill job#

STEP4) Before the job can be restarted, the following two lines must be added to the airbag.deploy.restart.k file:

*CHANGE_CURVE_DEFINITION
         1

STEP5) Now resubmit the job as follows using "r=" to specify the restart file:

sqsub -r 1h -q mpi --mpp=4G -n 8 -o ofile.%J lsdyna_d i=airbag.deploy.restart.k r=d3dump01

General Notes

Checking Job Status

To check the status of your job in the queue use the sqjobs command. On x86_64 systems you can check whether any of your jobs are queued on the license server use lstc_qrun. Its possible that sqsub will start your job but it will sit idle until enough license are available on the license server and the lstc_qrun command will reveal this:

[roberpj@hnd19:~/samples/lsdyna] lstc_qrun
Defaulting to server 1 specified by LSTC_LICENSE_SERVER variable
 
                     Running Programs
 
    User             Host          Program              Started       # procs
-----------------------------------------------------------------------------
hsnmoham    12208@orc271.orca.shar MPPDYNA          Mon Jan  7 18:17    24
 roberpj     9767@hnd15            LS-DYNA_971      Mon Jan  7 19:42     4
No programs queued

Checking License Details

At the time of this writing UWO is running on a 4cpu demo license as follows:

[roberpj@hnd19:~/samples/lsdyna]  lstc_qrun -R
Defaulting to server 1 specified by LSTC_LICENSE_SERVER variable
 
LICENSE INFORMATION
 
PROGRAM          EXPIRATION CPUS  USED   FREE    MAX | QUEUE
---------------- ----------      ----- ------ ------ | -----
LS-DYNA_971      05/31/2013          -    172    200 |     0
 roberpj     9767@hnd15              4
MPPDYNA_971      05/31/2013          0    172    200 |     0
LS-DYNA          05/31/2013          0    172    200 |     0
MPPDYNA          05/31/2013          -    172    200 |     0
 hsnmoham   12208@orc271.orca.sharcnet  24
                   LICENSE GROUP    28    172    200 |     0
 
PROGRAM          EXPIRATION CPUS  USED   FREE    MAX | QUEUE
---------------- ----------      ----- ------ ------ | -----
LS-OPT           05/31/2013          0    200    200 |     0
                   LICENSE GROUP     0    200    200 |     0

Legacy Version Instructions

The following binaries remain available on saw and orca for backward compatibility testing:

[roberpj@orc-login2:~] cd /opt/sharcnet/local/lsdyna
[roberpj@orc129:/opt/sharcnet/local/lsdyna] ls ls971*
ls971_d_R3_1    ls971_d_R4_2_1  ls971_s_R3_1    ls971_s_R4_2_1  ls971_s_R5_1_1
ls971_d_R4_2_0  ls971_d_R5_0    ls971_s_R4_2_0  ls971_s_R5_0

There are currently no sharcnet modules for these versions, hence jobs should be submitted as follows:

module load lsdyna
export PATH=/opt/sharcnet/local/lsdyna:$PATH
export LSTC_LICENSE_SERVER=XXXXX@license3.uwo.sharcnet
cp /opt/sharcnet/local/lsdyna/examples/airbag.deploy.k airbag.deploy.k
SERIAL JOB:  sqsub -q serial -r 1d -o ofile.%J ls971_d_R4_2_1 i=airbag.deploy.k
THREADED JOB:  sqsub -q threaded -n 4 -r 1d -o ofile.%J ls971_d_R4_2_1 ncpu=4 para=2 i=airbag.deploy.k

Note! the ls971_s_R3_1 and ls971_d_R3_1 binaries do not work, a fix is being looked for.

References

o LSTC LS-DYNA Homepage
http://www.lstc.com/lsdyna.htm